Differential binding cell-SELEX method to identify cell-specific aptamers using high-throughput sequencing

[1]  John G. Bruno,et al.  Aptamers in the Therapeutics and Diagnostics Pipelines , 2018, Theranostics.

[2]  Renan Valieris,et al.  Bioconda: sustainable and comprehensive software distribution for the life sciences , 2018, Nature Methods.

[3]  Khalid K. Alam,et al.  Poly-Target Selection Identifies Broad-Spectrum RNA Aptamers , 2018, bioRxiv.

[4]  H. Ulrich,et al.  Aptamers: novelty tools for cancer biology , 2018, Oncotarget.

[5]  John G. Bruno,et al.  Simple Methods and Rational Design for Enhancing Aptamer Sensitivity and Specificity , 2018, Front. Mol. Biosci..

[6]  Rolf Backofen,et al.  AptaSUITE: A Full-Featured Bioinformatics Framework for the Comprehensive Analysis of Aptamers from HT-SELEX Experiments , 2018, Molecular therapy. Nucleic acids.

[7]  Yuri Kotliarov,et al.  Assessment of Variability in the SOMAscan Assay , 2017, Scientific Reports.

[8]  John C. Chaput,et al.  Analysis of aptamer discovery and technology , 2017 .

[9]  J. Rossi,et al.  Aptamers as targeted therapeutics: current potential and challenges , 2016, Nature Reviews Drug Discovery.

[10]  L. Saal,et al.  Integrated molecular pathway analysis informs a synergistic combination therapy targeting PTEN/PI3K and EGFR pathways for basal-like breast cancer , 2016, BMC Cancer.

[11]  A. Evans,et al.  Efficient generation of patient-matched malignant and normal primary cell cultures from clear cell renal cell carcinoma patients: clinically relevant models for research and personalized medicine , 2016, BMC Cancer.

[12]  Ryan T. Strachan,et al.  Conformationally Selective RNA Aptamers Allosterically Modulate the β2-Adrenoceptor , 2016, Nature chemical biology.

[13]  Parashar Dhapola,et al.  QuadBase2: web server for multiplexed guanine quadruplex mining and visualization , 2016, Nucleic Acids Res..

[14]  I. Pabinger,et al.  A new measure for in vivo thrombin activity in comparison with in vitro thrombin generation potential in patients with hyper- and hypocoagulability , 2016, Clinical and Experimental Medicine.

[15]  Jørgen Kjems,et al.  Characterisation of aptamer–target interactions by branched selection and high-throughput sequencing of SELEX pools , 2015, Nucleic acids research.

[16]  Zhiming Zhang,et al.  Onset Time and Durability of Huntingtin Suppression in Rhesus Putamen After Direct Infusion of Antihuntingtin siRNA , 2015, Molecular therapy. Nucleic acids.

[17]  Phuong Dao,et al.  Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery , 2015, Nucleic acids research.

[18]  Khalid K. Alam,et al.  FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections , 2015, Molecular therapy. Nucleic acids.

[19]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[20]  James O McNamara,et al.  Cell-internalization SELEX: method for identifying cell-internalizing RNA aptamers for delivering siRNAs to target cells. , 2015, Methods in molecular biology.

[21]  J. Lis,et al.  New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization , 2014, Molecular therapy. Nucleic acids.

[22]  K. Flanigan,et al.  Targeted Exon Skipping to Correct Exon Duplications in the Dystrophin Gene , 2014, Molecular therapy. Nucleic acids.

[23]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[24]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[25]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[26]  Michael Famulok,et al.  Fluorescence-activated cell sorting for aptamer SELEX with cell mixtures , 2010, Nature Protocols.

[27]  Thomas Werner,et al.  Next generation sequencing in functional genomics , 2010, Briefings Bioinform..

[28]  D. Shangguan,et al.  Development of DNA aptamers using Cell-SELEX , 2010, Nature Protocols.

[29]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[30]  Yue Zhao,et al.  Inferring Binding Energies from Selected Binding Sites , 2009, PLoS Comput. Biol..

[31]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[32]  Ying-Fon Chang,et al.  Tenascin-C Aptamers Are Generated Using Tumor Cells and Purified Protein* , 2001, The Journal of Biological Chemistry.

[33]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[34]  J. Szostak,et al.  In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.